With the way I have this working right now, it would be kind of hard to make it shiny, because the event only checks to see if the species is in your party. I'd need a little help to be able to implement an event that would let you choose the specific party Pokémon to walk, and check for shininess on that Pokémon, because I'm still somewhat new.
For a bit of an update on things I've been doing, since I've been so quiet recently...
I've been working on a factions and reputation system that is based on variables and may or may not make it into the game. I normally don't mention these things, and I won't mention all the things I might do with it, because I don't want to get all of your hopes up for nothing.
But, as it stands, there are different factions, such as the lab workers or the teams, who will interact differently with the player depending on their rating of approval with that faction, from 0-100, with 50 being, "we don't know you, or we just don't care".
I was working on getting the lab in Forest Town to work with it.
Also... Your actions may have consequences. Unless I fry my own brain with implementing it. Right now, if you say you don't want to take the Pokédex, and you're serious about it... Well, you won't have a Pokédex for a while after that, and who knows when or if you'll get another chance to take one... >D
Anyway, thanks to everyone who thinks this game is worth continuing. It really makes my day when I read those kind of comments.